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Author SHA1 Message Date
Greg Von Kuster f6b05fea77 Change function signatures for several utility functions that used to require trans but now only need app. 2014-05-21 09:55:12 -04:00
Greg Von Kuster 9602fb498a Merged next-stable 2014-05-20 17:27:29 -04:00
Greg Von Kuster 3bc5de168e Fix for rendering the metadata about a tool contained in a repository installed from the Tool Shed into Galaxy. 2014-05-20 17:27:00 -04:00
Greg Von Kuster f4fee7d3cb Add a repository registry to the Tool Shed to keep in-memory information about repositories. This will significantly improve some page rendering in the tool shed, specifically the current main Categories splash page. This registry will provide filtered certification information for the planned Tool Shed splash page which will be rendered with Javascript. The Tool Shed's install and test framework still needs to be enhanced to update this registry during install and test runs. 2014-05-20 17:18:14 -04:00
Greg Von Kuster 9e81d4efeb Only load the tool panel if in Galaxy. 2014-05-20 17:13:26 -04:00
John Chilton abe9778797 Document install_database_connection in universe_wsgi.ini. 2014-05-20 16:07:43 -05:00
John Chilton 20b8c23ab3 Merge next-stable. 2014-05-20 15:31:43 -05:00
John Chilton e866dc6a70 Fix up job_conf.xml env element logging. 
Now works with all runners.
 2014-05-20 15:31:14 -05:00
John Chilton efdafb2f68 Enable job metrics by default. 
They should work with all stock Galaxy runners now.
 2014-05-20 15:31:14 -05:00
Dannon Baker a7d7b70d53 Merge next-stable. 2014-05-20 12:06:21 -04:00
Dannon Baker 33e9565bd2 Clarify default option (no quotes) for amqp_internal_connection 2014-05-20 12:06:07 -04:00
Dannon Baker 7657a2effe Merge next-stable. 2014-05-20 11:55:54 -04:00
Dannon Baker 034a1be99f When using AMQP, if the AMQP server goes down this will now more nicely catch the Connection refused error in send_control_task 2014-05-20 11:55:24 -04:00
Daniel Blankenberg 7bb08364db merge next-stable 2014-05-20 10:32:31 -04:00
Daniel Blankenberg b616072582 Fix for reports app's default database/sqlite settings. Most of the reports app will still not work with sqlite however. 2014-05-20 10:32:13 -04:00
Daniel Blankenberg 2e61615712 merge next-stable 2014-05-20 10:18:49 -04:00
Daniel Blankenberg ca7c93c729 To maintain previous behavior, list custom genome build names first. 2014-05-20 10:18:28 -04:00
Daniel Blankenberg 1495c2ac0c merge next-stable 2014-05-20 10:01:53 -04:00
Daniel Blankenberg 49e1e48a59 Cleanup for dbkey handling. 2014-05-20 10:01:28 -04:00
Dannon Baker 7261896dfc Merge next-stable 2014-05-19 19:54:25 -04:00
Dannon Baker 33e132bf03 Additional anyjson requires (appeared to cause Toolshed issues for Greg) 2014-05-19 19:54:05 -04:00
Dannon Baker 9f1e49e8be Merge from next-stable. 2014-05-19 18:58:28 -04:00
Dannon Baker fceadaf1f2 Kombu also requires ordereddict backport to support python2.6, more eggs. 2014-05-19 18:58:13 -04:00
Dannon Baker 020edce820 Merge next-stable 2014-05-19 18:12:05 -04:00
Dannon Baker c05bef0908 Add conditional requirement of importlib for python 2.6/kombu. 2014-05-19 18:11:52 -04:00
Dannon Baker 79abc4243c Merge next-stable. 2014-05-19 17:47:36 -04:00
Dannon Baker e878d8ac5d Fix get_chrom_info to take (and use) the tool in question. 2014-05-19 17:47:20 -04:00
Dannon Baker 748bb5657b Merge from next-stable. 2014-05-19 17:44:25 -04:00
Dannon Baker 3e66202c08 Fix (kind of a guess as to the intended functionality) input_dbkey error. 2014-05-19 17:42:05 -04:00
John Chilton f678714813 Merge next-stable. 2014-05-19 16:18:31 -05:00
John Chilton a0471e8705 HACK: Fix circular dependency non-sense related to tools and dataset collections. 
https://gist.github.com/jmchilton/6e19d248002b1080e8ba.
 2014-05-19 16:18:02 -05:00
Dannon Baker c850209752 Merge from next-stable. 2014-05-19 16:56:28 -04:00
Dannon Baker 8c4a0f096e Initial internal control message queue for IPC implementation. Needs significant refactoring, as noted in some TODOs, but this is a minimally functional version so it makes the next-stable cutoff. Currently only handles reloading tools and data tables, but adding additional tasks is simple and should be straightforward. 2014-05-19 16:56:08 -04:00
Dave Bouvier b433151854 Merge with next-stable. 2014-05-19 16:39:25 -04:00
Dave Bouvier e86191b617 Remove migrated tools from main's tool_conf.xml 2014-05-19 16:38:58 -04:00
Nate Coraor 8bcf293eff Open next-stable for upcoming June release. 2014-05-19 15:55:21 -04:00
Daniel Blankenberg 0c1efa4831 Fix for tool shed handling new GenomeBuilds manager. 2014-05-19 15:35:58 -04:00
Daniel Blankenberg 75aa0a2a9b First pass at allowing dbkeys / genome builds to be loaded from Tool Data Tables. 2014-05-19 15:08:26 -04:00
John Chilton 448e345119 Pack scripts. 2014-05-19 13:38:21 -05:00
John Chilton 121c481411 Don't show different multi-run option button if only one option. 2014-05-19 13:36:49 -05:00
Dave Bouvier 9b8e5dc885 Remove migrated tools from the tool conf files. 2014-05-19 13:02:11 -04:00
Dave Bouvier a3018feb02 Migrate 22 tools from the distribution to the tool shed. 2014-05-19 13:01:46 -04:00
John Chilton 650626db4e More performant database interaction during collection creation. 2014-05-19 12:15:48 -05:00
John Chilton 3cd33a70f2 Rework, improve validation of dataset creation requests. 
Being more thorough fixes some potential security problems and will allow some performance optimizations I'm planning.
 2014-05-19 11:51:07 -05:00
Dannon Baker ea906a5a6f Followup from commentary on PR394, cleaned up incorrect log.exception usage in base controller. 2014-05-19 12:47:10 -04:00
Dannon Baker 5b77b623ad Merge PR394 from stable. 2014-05-19 12:39:59 -04:00
Nicola Soranzo b04eb27990 Fix for "'HistoryTagsController' object has no attribute 'security_check'". 
Trying to access /api/histories/$history_id/tags gives this error:

Execption in get_object check for History 1723db999e478a37: 'HistoryTagsController' object has no attribute 'security_check'
Traceback (most recent call last):
  File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 233, in get_object
    check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted )
  File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 131, in get_object
    self.security_check( trans, item, check_ownership, check_accessible )
AttributeError: 'HistoryTagsController' object has no attribute 'security_check'

The same happens for workflow tags.
 2014-05-19 18:03:21 +02:00
John Chilton 9ca839fca8 More reworking of job logging. 
Drop now duplicated log message in drmaa, condor, cli, etc.... Have local job runner report which job script it is running - but log it as a job script. For each job runner log the full command-line which includes dependency resolution and not the base version produced directly by the tool and use the old format from the external runners.
 2014-05-19 11:02:59 -05:00
John Chilton b1d39bbfb9 Improved job logging. 
Remove now less useful local runner command-line log statement (still contend it will be valuable for debugging purposes to be able to tweak and rerun the exact script - but point taken :)) . Remove stray statement added in ff4b5fe. Add new logging statement that logs just the base command-line produced by tools for all job runners. Add little note to runners/__init__.py about how to produce an extended command-line logging (with metadata handling, dependencies, and from_work_dir handling).
 2014-05-19 10:16:12 -05:00
Daniel Blankenberg 4fdfc45156 Fixes for genomespace exporter recieving UnvalidatedValue objects. 2014-05-19 10:17:36 -04:00